Clinical application of amplicon-based next-generation sequencing in cancer

Next-generation sequencing (NGS) technology has revolutionized genomic research by decreasing the cost of sequencing while increasing the throughput. The focus now is on potential clinical applications of NGS technology for diagnostics and therapeutics. Clinical applications of NGS in cancer can detect clinically actionable genetic/genomic alterations that are critical for cancer care. These alterations can be of diagnostic, prognostic, or therapeutic significance. In certain cancers, patient risk and prognosis can be predicted based on the mutation profile identified by NGS. Many targeted therapies have been developed for cancer patients who bear specific mutations; however, choosing the right NGS technique for the appropriate clinical application can be challenging, especially in clinical oncology, where the material for NGS tests is often limited and the turnaround time (TAT) for cancer tests is constrained to a few days. Currently, amplicon-based NGS approaches have emerged as the best fit for clinical oncology. In this review, we focus on amplicon-based library preparation, sequencing, sequence data alignment and annotation, and post-analytic interpretation and reporting.